phantasm
PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes (by dr-joe-wirth)
pyani
Application and Python module for average nucleotide identity analyses of microbes. (by widdowquinn)
| phantasm | pyani | |
|---|---|---|
| 2 | 1 | |
| 24 | 203 | |
| - | 1.5% | |
| 8.6 | 7.2 | |
| over 1 year ago | about 2 months ago | |
| Python | Python | |
| MIT License | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
phantasm
Posts with mentions or reviews of phantasm.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-04-02.
- Is there any way to easily create a docker image that has both python and R?
-
PHANTASM: new software for microbial taxonomy
The easiest way to try it out PHANTASM is to use the Docker image. The source code is also available on github.
pyani
Posts with mentions or reviews of pyani.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-10-20.
-
MAFFT Alignment taking longer than expected
But to help you along, one would chop up the genomes into smaller bits to robustly handle potential re-arrangements. A classic tool to do so, is the MUMMER algorithm, which for your purpose is nicely implemented here: https://github.com/widdowquinn/pyani
What are some alternatives?
When comparing phantasm and pyani you can also consider the following projects:
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
drep - Rapid comparison and dereplication of genomes
misp-taxonomies - Taxonomies used in MISP taxonomy system and can be used by other information sharing tool.
fideslang - Open-source description language for privacy to declare data types and data behaviors in your tech stack in order to simplify data privacy globally. Supports GDPR, CCPA, LGPD and ISO 19944.